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Package 244/631HostnameOS / ArchBUILDCHECKBUILD BIN
GeneRegionScan 1.15.5
Lasse Folkersen
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneRegionScan
Last Changed Rev: 71244 / Revision: 72575
Last Changed Date: 2012-11-15 01:52:05 -0800 (Thu, 15 Nov 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GeneRegionScan
Version: 1.15.5
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GeneRegionScan_1.15.5.tar.gz
StartedAt: 2013-01-16 02:49:26 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 02:54:43 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 316.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneRegionScan.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GeneRegionScan.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneRegionScan/DESCRIPTION’ ... OK
* this is package ‘GeneRegionScan’ version ‘1.15.5’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GeneRegionScan’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.4Mb
  sub-directories of 1Mb or more:
    exec  19.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotOnGene,ExpressionSet: warning in plot.default(1, type = "n", xlab =
  "bp", ylab = ylab, frame = FALSE, xlim = xlim, ylim = ylim, main =
  paste("Expression of probes"), cex.main = 1): partial argument match
  of 'frame' to 'frame.plot'
plotCoexpression,ExpressionSet: no visible binding for global variable
  ‘interval’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
geneRegionScan   73.472 14.904  88.406
plotCoexpression 51.780 15.381  67.162
plotOnGene       18.549  0.004  18.554
exonStructure    11.313  0.032  11.350
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GeneRegionScan.Rcheck/00check.log’
for details.

GeneRegionScan.Rcheck/00install.out:

* installing *source* package ‘GeneRegionScan’ ...
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GeneRegionScan.Rnw’ 
** testing if installed package can be loaded

* DONE (GeneRegionScan)

GeneRegionScan.Rcheck/GeneRegionScan-Ex.timings:

nameusersystemelapsed
addSnpPdata0.0080.0000.007
checkForFileInPath0.0280.0040.127
doProbeLinear2.3760.0202.397
doProbeTTest0.5640.0120.579
exampleProbeLevelSet0.2680.0120.280
excludeDoubleMatchingProbes0.0120.0000.009
exonStructure11.313 0.03211.350
findProbePositions0.8320.0080.839
findSequenceInGenome0.2400.0040.241
geneRegionScan73.47214.90488.406
getLocalMetaprobeIntensities0.0000.0080.008
getLocalProbeIntensities0.0000.0080.006
getMetaprobesetsFromRegionOfInterest0.0000.0080.007
getProbeLevelAnnotationForExonArrays0.0000.0080.006
getProbesetsFromMetaprobeset0.0000.0080.006
getProbesetsFromRegionOfInterest0.0000.0080.006
getSequence0.0160.0120.029
getServerProbeIntensities0.0080.0200.028
plotCoexpression51.78015.38167.162
plotOnGene18.549 0.00418.554
readGeneInput0.0040.0000.005
translateSampleNames0.0640.0000.067